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from typing import Any, Tuple, Union
import MySQLdb
def get_trait_csv_sample_data(conn: Any,
trait_name: int, phenotype_id: int) -> str:
"""Fetch a trait and return it as a csv string"""
__query = ("SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',', "
"ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) as 'Data' "
",ifnull(ca.Name, 'x') as 'CaseAttr', "
"ifnull(cxref.value, 'x') as 'Value' "
"FROM PublishFreeze pf "
"JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId "
"JOIN PublishData pd ON pd.Id = px.DataId "
"JOIN Strain st ON pd.StrainId = st.Id "
"LEFT JOIN PublishSE ps ON ps.DataId = pd.Id "
"AND ps.StrainId = pd.StrainId "
"LEFT JOIN NStrain ns ON ns.DataId = pd.Id "
"AND ns.StrainId = pd.StrainId "
"LEFT JOIN CaseAttributeXRefNew cxref ON "
"(cxref.InbredSetId = px.InbredSetId AND "
"cxref.StrainId = st.Id) "
"LEFT JOIN CaseAttribute ca ON ca.Id = cxref.CaseAttributeId "
"WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name")
case_attr_columns = set()
csv_data = {}
with conn.cursor() as cursor:
cursor.execute(__query, (trait_name, phenotype_id))
for data in cursor.fetchall():
if data[1] == "x":
csv_data[data[0]] = None
else:
sample, case_attr, value = data[0], data[1], data[2]
if not csv_data.get(sample):
csv_data[sample] = {}
csv_data[sample][case_attr] = None if value == "x" else value
case_attr_columns.add(case_attr)
if not case_attr_columns:
return ("Strain Name,Value,SE,Count\n" +
"\n".join(csv_data.keys()))
else:
columns = sorted(case_attr_columns)
csv = ("Strain Name,Value,SE,Count," +
",".join(columns) + "\n")
for key, value in csv_data.items():
if not value:
csv += (key + (len(case_attr_columns) * ",x") + "\n")
else:
vals = [str(value.get(column, "x")) for column in columns]
csv += (key + "," + ",".join(vals) + "\n")
return csv
return "No Sample Data Found"
def get_sample_data_ids(conn: Any, publishxref_id: int,
phenotype_id: int,
strain_name: str) -> Tuple:
strain_id, publishdata_id, inbredset_id = None, None, None
with conn.cursor() as cursor:
cursor.execute("SELECT st.id, pd.Id, pf.InbredSetId "
"FROM PublishData pd "
"JOIN Strain st ON pd.StrainId = st.Id "
"JOIN PublishXRef px ON px.DataId = pd.Id "
"JOIN PublishFreeze pf ON pf.InbredSetId "
"= px.InbredSetId WHERE px.Id = %s "
"AND px.PhenotypeId = %s AND st.Name = %s",
(publishxref_id, phenotype_id, strain_name))
if _result := cursor.fetchone():
strain_id, publishdata_id, inbredset_id = _result
return (strain_id, publishdata_id, inbredset_id)
def update_sample_data(conn: Any, # pylint: disable=[R0913]
trait_name: str,
strain_name: str,
phenotype_id: int,
value: Union[int, float, str],
error: Union[int, float, str],
count: Union[int, str]):
"""Given the right parameters, update sample-data from the relevant
table."""
strain_id, data_id, _ = get_sample_data_ids(
conn=conn, publishxref_id=trait_name,
phenotype_id=phenotype_id, strain_name=strain_name)
updated_published_data: int = 0
updated_se_data: int = 0
updated_n_strains: int = 0
with conn.cursor() as cursor:
# Update the PublishData table
if value == "x":
cursor.execute(("DELETE FROM PublishData "
"WHERE StrainId = %s AND Id = %s")
% (strain_id, data_id))
updated_published_data = cursor.rowcount
else:
cursor.execute(("UPDATE PublishData SET value = %s "
"WHERE StrainId = %s AND Id = %s"),
(value, strain_id, data_id))
updated_published_data = cursor.rowcount
if not updated_published_data:
cursor.execute(
"SELECT * FROM "
"PublishData WHERE StrainId = "
"%s AND Id = %s" % (strain_id, data_id))
if not cursor.fetchone():
cursor.execute(("INSERT INTO PublishData (Id, StrainId, "
" value) VALUES (%s, %s, %s)") %
(data_id, strain_id, value))
updated_published_data = cursor.rowcount
# Update the PublishSE table
if error == "x":
cursor.execute(("DELETE FROM PublishSE "
"WHERE StrainId = %s AND DataId = %s") %
(strain_id, data_id))
updated_se_data = cursor.rowcount
else:
cursor.execute(("UPDATE PublishSE SET error = %s "
"WHERE StrainId = %s AND DataId = %s"),
(None if error == "x" else error,
strain_id, data_id))
updated_se_data = cursor.rowcount
if not updated_se_data:
cursor.execute(
"SELECT * FROM "
"PublishSE WHERE StrainId = "
"%s AND DataId = %s" % (strain_id, data_id))
if not cursor.fetchone():
cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, "
" error) VALUES (%s, %s, %s)") %
(strain_id, data_id,
None if error == "x" else error))
updated_se_data = cursor.rowcount
# Update the NStrain table
if count == "x":
cursor.execute(("DELETE FROM NStrain "
"WHERE StrainId = %s AND DataId = %s" %
(strain_id, data_id)))
updated_n_strains = cursor.rowcount
else:
cursor.execute(("UPDATE NStrain SET count = %s "
"WHERE StrainId = %s AND DataId = %s"),
(count, strain_id, data_id))
updated_n_strains = cursor.rowcount
if not updated_n_strains:
cursor.execute(
"SELECT * FROM "
"NStrain WHERE StrainId = "
"%s AND DataId = %s" % (strain_id, data_id))
if not cursor.fetchone():
cursor.execute(("INSERT INTO NStrain "
"(StrainId, DataId, count) "
"VALUES (%s, %s, %s)") %
(strain_id, data_id, count))
updated_n_strains = cursor.rowcount
return (updated_published_data,
updated_se_data, updated_n_strains)
def delete_sample_data(conn: Any,
trait_name: str,
strain_name: str,
phenotype_id: int):
"""Given the right parameters, delete sample-data from the relevant
table."""
strain_id, data_id, _ = get_sample_data_ids(
conn=conn, publishxref_id=trait_name,
phenotype_id=phenotype_id,
strain_name=strain_name)
deleted_published_data: int = 0
deleted_se_data: int = 0
deleted_n_strains: int = 0
with conn.cursor() as cursor:
# Delete the PublishData table
try:
# Only run if the strain_id and data_id exist
if strain_id and data_id:
cursor.execute(("DELETE FROM PublishData "
"WHERE StrainId = %s AND Id = %s")
% (strain_id, data_id))
deleted_published_data = cursor.rowcount
# Delete the PublishSE table
cursor.execute(("DELETE FROM PublishSE "
"WHERE StrainId = %s AND DataId = %s") %
(strain_id, data_id))
deleted_se_data = cursor.rowcount
# Delete the NStrain table
cursor.execute(("DELETE FROM NStrain "
"WHERE StrainId = %s AND DataId = %s" %
(strain_id, data_id)))
deleted_n_strains = cursor.rowcount
except Exception as e: #pylint: disable=[C0103, W0612]
conn.rollback()
raise MySQLdb.Error
conn.commit()
cursor.close()
cursor.close()
return (deleted_published_data,
deleted_se_data, deleted_n_strains)
def insert_sample_data(conn: Any, # pylint: disable=[R0913]
trait_name: str,
strain_name: str,
phenotype_id: int,
value: Union[int, float, str],
error: Union[int, float, str],
count: Union[int, str]):
"""Given the right parameters, insert sample-data to the relevant table.
"""
inserted_published_data, inserted_se_data, inserted_n_strains = 0, 0, 0
strain_id, data_id = get_sample_data_ids(
conn=conn, publishxref_id=trait_name,
phenotype_id=phenotype_id,
strain_name=strain_name)
with conn.cursor() as cursor:
try:
# Return early if an insert already exists!
cursor.execute("SELECT Id FROM PublishData where Id = %s "
"AND StrainId = %s",
(data_id, strain_id))
if cursor.fetchone(): # This strain already exists
return (0, 0, 0)
# Insert the PublishData table
cursor.execute(("INSERT INTO PublishData (Id, StrainId, value)"
"VALUES (%s, %s, %s)"),
(data_id, strain_id, value))
inserted_published_data = cursor.rowcount
# Insert into the PublishSE table if error is specified
if error and error != "x":
cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, "
" error) VALUES (%s, %s, %s)") %
(strain_id, data_id, error))
inserted_se_data = cursor.rowcount
# Insert into the NStrain table
if count and count != "x":
cursor.execute(("INSERT INTO NStrain "
"(StrainId, DataId, count) "
"VALUES (%s, %s, %s)") %
(strain_id, data_id, count))
inserted_n_strains = cursor.rowcount
except Exception: # pylint: disable=[C0103, W0612]
conn.rollback()
raise MySQLdb.Error
return (inserted_published_data,
inserted_se_data, inserted_n_strains)
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